You probably need to use IsPrimary like in the below code snippt

var nodeRelations = _relationRepository.GetParents<NodeEntryRelation>(entryContentReference).ToList();

            var primaryRelation = nodeRelations.FirstOrDefault(x => x.IsPrimary);

            if (primaryRelation != null)
            {
                var thisRelationContentReference = _referenceConverter.GetContentLink(primaryRelation.Parent.ID, CatalogContentType.CatalogNode, primaryRelation.Parent.WorkID);
                var nodeContentBase = _contentLoader.Get<NodeContentBase>(thisRelationContentReference);
                return nodeContentBase.ContentLink;
            }

My memory is a bit rusty but yes it is a known issue. That will only return the linked node. You need to get the node content and use ParentLink to get the true parent node. 
IsPrimary is only for node entry relation btw